1nterceptor can probably give you better suggestions for commuter lights. I have the luxury of the greenway during daylight hours, and well-lit surface streets in the evenings, so I just have
these guys blinking all over my bike.
Your rear lights can be normal blinkies. Planet Bike has the Super Flash LED which is great, and practically impossible to ignore by motorists. As for your front lights, you can get an equivalent LED light, or if you want some serious wattage, invest in an HID or something similar. Chainlove and Bonktown (usually the former, sometimes the latter) will have HID lights pop up every now and again. Be patient and you could score one for a deep discount, or you could look for one on ebay.
As for parts getting stolen, read up in threads here on how to lock up your bike properly, or just google it. My own method is to use a Kryptonite mini U-lock on the frame, Pinhead skewers on the wheels, and to use wax to stuff ball bearings into any allen screws holding down parts (quill stem, derailleurs, brakes, etc.) Using candle wax makes it easy for you to pry out the bearing when you need to make adjustments or swap out parts, but most thieves will be deterred by having to go through that procedure. Plus they don't know whether or not you've epoxied it as opposed to using simple wax.